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|Title:||Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs|
Nielsen, Rasmus O.
Coffey, Mary F.
De la Rúa, Pilar
Drazic, M. Maja
Matray, Enikö Sz.
Nikolenko, Alexei G.
Pinto, M. Alice
Poskryakov, Aleksandr V.
Sharipov, Aglyam Y.
Soysal, M. Ihsan
Meixner, Marina D.
|Keywords:||Insects -- Malta|
Hymenoptera -- Malta
Apidae -- Malta
Apis (Insects) -- Malta
Honeybee -- Malta
Honeybee -- Conservation
Bees -- Conservation
Biodiversity -- Malta
|Citation:||Momeni, J., Parejo, M., Nielsen, R. O., Langa, J., Montes, I., Papoutsis, L., ... & Estonba, A. (2021). Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs. BMC Genomics, 22(1), 1-12.|
|Abstract:||Background: With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds
a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered
by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for
subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled
across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative
SNPs for ancestry inference.|
Results: Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof.
Conclusions: The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.
|Appears in Collections:||Scholarly Works - InsESRSF|
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